Author Archives: Pedro J Aphalo

About Pedro J Aphalo

I am an university lecturer in physiological plant ecology and principal investigator at the Department of Biosciences of the University of Helsinki.

However good data looks at first sight, check it!

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Introduction

I will tell today two true stories, one old and one very recent. The point that I want to make today is that one should never blindly trust the results of measurements. This applies in general, but both examples I will present have to do with measurements made with instruments, more specifically with measuring UV-B radiation in experiments using lamps.

A case from nearly 20 years ago

Researcher A received a new very good spectroradiometer from the manufacturer and used it to set the UVB output from the lamps.

Researcher B had access to an old spectroradiometer that could measure only a part of the UVB spectrum. He knew this, and measured the part of the spectrum that was possible to measure, and extrapolated the missing part from published data. He also searched the literature and compared his estimates to how the same lamps had been used earlier.

Researcher A was unlucky enough that because of a mistake at the factory, the calibration of the new instrument was wrong by about a factor of 10. She did not notice until after the experiment was well under way, but before publication. The harm was that the results were less relevant than what had been the aim, but no erroneous information was published.

Researcher B was able able to properly measure the UVB irradiance after the experiment was well under way, and he found that the treatment was within a small margin of what he had aimed.

A case I discovered just a few days ago

A recently published paper concluded that they had obtained evidence that a low and ecologically relevant dose of UVB on a single day was able to elicit a large response in the plants. From the description of the lamps used, the distance to the plants and the time that the lamps were kept switched on is easy to estimate that in fact they had applied a dose that was at least 15 or 20 times what they had measured and reported in the paper. Coupled to a low level of visible light this explains why they observed a large response from the plants! Neither the authors, reviewers, nor the editor had noticed the error! [added on 8 October] I read a few other papers on similar subjects from the same research group and the same problem seems to also affect them. I will try to find out the origin of the discrepancy, and report here what I discover.

[added on 26 October]
 I have contacted three of the authors. They have confirmed the problem. Cause seems to have been that the researchers did not notice that the calibration they used had been expressed in unusual units by the manufacturer. The authors are concerned and are checking how large the error was, but first comparative measurements suggest that the reported values were underestimated by a factor of at least 20 times.

About this case, I do not yet know the whole story, but evidently it yielded a much worse result: The publication of several articles with wrong data and wrong conclusions.

Take home message

Whenever and whatever you measure, or when you use or assess non-validated data from any source, unless you know very well from experience what to expect, check the literature for ballpark numbers. In either case, if your data differ significantly from expectations try to find an explanation for the difference before you accept the data as good. You will either find an error or discover something new.

CFCs, the ozone layer and global change

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Bar graphs.

Figure from NASA’s Ozone Hole Watch showing changes in the ozone hole since 1979 until last year.

I guess most people reading this blog already know about the role of CFCs in the thinning of the ozone layer and its extreme manifestation the “ozone hole”. (If not you will find explanations here and here and ozone depletion maps here, and information on the Montreal protocol here and here.)

An article by Prof. Nigel Paul published in the The Conversation highlights the success of the protocol.

However, what fewer people know is that CFCs are potent “greenhouse gases”, and a recent article discusses why of all measures taken up to day, what has most significantly contributed to slowing-down global warming is the Montreal protocol. In my view, to a large extent this just shows how little progress has been achieved in reducing emissions of other “greenhouse gases” like carbon dioxide. A recent article in The Economist highlights this.

 

Biosophical society

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I guess most of you have seen thisBS-poster poster tacked on the elevators walls and on the front door of Biocenter 3. If you are a student, or a researcher and you aim at understanding science, then the events organized by the society will surely broaden your view. At least from time to time, we all need to stop, and spend some time pondering the deeper questions about Biology. This helps in many ways: 1) it will make us think about things and assumptions we normally take for granted, 2) it will allow us to put our own research in a much broader context, which could reveal either unsuspected implications or logical flaws, 3) hopefully they will lift to some extent our blindness to the “logic” behind research in other disciplines, allowing us to see new patterns and connections. The current group of participants comes from several different disciplines and have different research backgrounds which should make the discussions particularly interesting for everybody.

I will myself participate, and chair one session some time in November.

For the programme and additional infrmation see the society’s own web site.

For info or booking a date, email Matan.Shenhav@helsinki.fi

 

Talking plants

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This layman’s introduction to plant-plant communication in Quanta on-line magazine is interesting both in relation to the phenomena studied and how science works. Nowadays that plants communicate with each other is widely accepted, but several types of communication are still controversial and not all available evidence is as strong as one would wish. Consequently, it is a very exciting field and time to do research about plant-plant interactions, including communication!

“Reproducible research” is a hot question

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I have long been interested in the question of reproducible research and as a manuscript author, reviewer and more recently, editor, have attempted to make sure that no key information was missing and that methods were described in full detail and, of course, valid.

Although the problem has always existed, I think that in recent years papers and reports with badly described methods have become more frequent. I think that there are many reasons for this: 1) the pressure to publish quickly and frequently as a condition for career advance, 2) the overload on reviewers work’ and the pressure from journals to get manuscript reviews submitted within a few days’ time, 3) the stricter and stricter rules of journals about maximum number of “free” pages, and 4) the practice by some journals of publishing methods at the end of the papers or in smaller typeface, implying that methods are not important for most readers, and irrelevant for understanding the results described (which is a false premise).

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